Normally these programs run 'outside' your applications, and launch other applications as necessary to perform tasks - they don't, generally, take actions within those applications. They can sometimes interact with those applications to some degree by sending messages (e.g Intents in Android) or by communicating via a web API.
The problem you face with games is that they are not set up to receive this sort of input, at all. Most do not expose any sort of external API or interface, and any that do have their own proprietary ones. The games are typically driven only by input devices; keyboard, mouse, touch screen, etc. That is a much lower level than a digital assistant would normally operate at, and presents various problems (e.g. clashes with 'real' input devices, synchronising inputs that must be performed concurrently or sequentially, distinguishing inputs for the assistant from inputs for the game). But the biggest problem is that although these are the inputs shared across all games, they're not 'commands' in the semantic sense, and therefore the concept of "most used commands" may not make sense at this level.